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THE PLANE OF ONE BASE PAIR STACKS OVER THE OTHER IN DOUBLE HELIX.THIS CONFERS MORE STABILITY OF HELICAL STRUCTURE FOR DNA.HOW IS IT POSSIBLE?
DNA is usually a double-helix and has two strands running in opposite directions. (There are some examples of viral DNA which are single-stranded). Each chain is a polymer of subunits called nucleotides (hence the name polynucleotide).

Each strand has a backbone made up of (deoxy-ribose) sugar molecules linked together by phosphate groups. The 3' C of a sugar molecule is connected through a phosphate group to the 5' C of the next sugar. This linkage is also called 3'-5' phosphodiester linkage. All DNA strands are read from the 5' to the 3' end where the 5' end terminates in a phosphate group and the 3' end terminates in a sugar molecule. Each sugar molecule is covalently linked to one of 4 possible bases (Adenine, Guanine, Cytosine and Thymine). A and G are double-ringed larger molecules (called purines); C and T are single-ringed smaller molecules (called pyrimidines).

In the double-stranded DNA, the two strands run in opposite directions and the bases pair up such that A always pairs with T and G always pairs with C. The A-T base-pair has 2 hydrogen bonds and the G-C base-pair has 3 hydrogen bonds. The G-C interaction is therefore stronger (by about 30%) than A-T, and A-T rich regions of DNA are more prone to thermal fluctuations. The bases are oriented perpendicular to the helix axis. They are hydrophobic in the direction perpendicular to the plane of the bases (cannot form hydrogen bonds with water). The interaction energy between two bases in a double-helical structure is therefore a combination of hydrogen-bonding between complementary bases, and hydrophobic interactions between the neighboring stacks of base-pairs.

Even in the single-stranded state, the bases prefer to be stacked (like the steps of a spiral staircase if the bases are identical) and a single-stranded chain can also have regions of helical conformation.

The backbone of polynucleotides are highly charged (1 unit negative charge for each phosphate group; 2 negative charges per base-pair). If there is no salt in the surrounding medium, there is a strong repulsion between the two strands and they will fall apart. Therefore counter-ions are essential for the double-helical structure. Counter-ions shield the charges on the sugar-phosphate backbone. They may also contribute to an attractive interaction from fluctuating counter-ions around the backbone, similar to the Van der Waals interactions for fluctuating induced dipoles.


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